4.3 Conclusion
According to eDNA data, downstream ecosystems are the most species-rich.
They are also the most threatened, facing diffuse and cumulated threats
from upstream, and located in the most human-impacted areas (populated
areas, agricultural plains, industrial effluents…). Our eDNA
results highlight very important conservation issues for species
downstream of major rivers. In a context of biodiversity erosion and
declining populations sizes, it seems essential to implement consistent
conservation policies for downstream species, which are currently
insufficiently considered by naturalists and managers alike due to the
difficulty of access to these environments.
eDNA analyses, with an optimal protocol, have the potential of providing
not only ”presence”, but also ”absence” data. Using standardized methods
it becomes now possible to reliably document both the progression of
invasive species, as well as range contractions of endangered species.
Large-scale and long-term eDNA metabarcoding surveys clearly represent a
valuable tool for preserving and monitoring freshwater bivalves.
However, regarding the poorly known species, it should be kept in mind
that what we present here is 16S haplotypes distribution. They may not
reflect the actual distribution of species as further studies may
jeopardize the current state-of-the-art of molecular taxonomy. This is
just an eDNA point of view.
Acknowledgements
The development of the eDNA analysis method for bivalves was carried out
jointly by Caracol NGO, Spygen company and Biotope consultancy. The
Office Français de la Biodiversité and the Direction Régionale de
l’Environnement, de l’Aménagement et du Logement d’Occitanie contributed
to its financing. The data presented here includes work carried out by
Biotope and Aquascop consultancies, Caracol NGO, SpyGen, the Compagnie
Nationale du Rhône, the Regional Natural Park of Limousin, the
Conservatoires d’Espaces Naturels Midi-Pyrénées and Nouvelle Aquitaine,
the LIFE + Giant Freshwater Mussel program, GRT Gaz, Voies Navigables de
France, EPTB Vilaine, CPIE Loire-Anjou for the main studies. The DREAL
Grand Est, Nouvelle Aquitaine, Occitanie and the DDT du Tarn also
financed part of the studies. We would also like to thank all those who
participated in the sampling and laboratory analysis of the samples, in
particular Pascal Irz (OFB), Laurent Philippe (Biotope), Mathieu Saget
(Aquascop), Mathieu Charneau (OFB).
This research was also developed under ConBiomics: the missing approach
for the Conservation of Freshwater Bivalves Project Nº
NORTE-01-0145-FEDER-030286, co-financed by COMPETE 2020, Portugal 2020
and the European Union through the ERDF, and by Portuguese Foundation
for Science and Technology (FCT) through national funds.
References
Adam, B. (2010). L’Anodonte chinoise Sinanodonta woodiana (Lea,
1834) (Mollusca, Bivalvia, Unionidae) : une espèce introduite qui
colonise le bassin Rhône-Méditerranée. MalaCo , 6, 278-287.
Bij de Vaate, A., & Beisel J.-N. (2011). Range expansion of the quagga
mussel Dreissena rostriformis bugensis (Andrusov, 1897) in
Western Europe: first observation from France. Aquatic Invasions,6(Suppl. 1), 71–74. doi: 10.3391/ai.2011.6.S1.016
Bouchet, P. (2002). Mollusques terrestres et aquatiques de France: un
nouveau référentiel taxonomique, un nouveau départ, de nouvelles
perspectives. In G. Falkner, Th. E. J. Ripken, & M. Falkner (Eds.),Mollusques continentaux de France ; liste de référence annotée et
bibliographie (pp. 5-20). Paris, Patrimoines Naturels 52.
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., & Coissac
E. (2016). obitools: a unix-inspired software package for DNA
metabarcoding. Molecular Ecology Resources, 16, 176–182. doi:
10.1111/1755-0998.12428
Breton, S., Doucet-Beaupré, H., Stewart, D., Hoeh W., & Blier, P.
(2007). The unusual system of doubly uniparental inheritance of mtDNA:
Isn’t one enough? Trends in genetics, 23, 465-74. doi:
10.1016/j.tig.2007.05.011.
Darling, J. A., & Mahon, A. R. (2011). From molecules to management:
Adopting DNA-based methods for monitoring biological invasions in
aquatic environments. Environmental Research, 111, 978–988. doi:
10.1016/j.envres.2011.02.001
Darwall, W., Carrizo, S., Numa, C., Barrios, V., Freyhof, J., & Smith,
K. (2014). Freshwater Key Biodiversity Areas in the Mediterranean
Basin Hotspot: Informing species conservation and development planning
in freshwater ecosystems . Retrieved from IUCN website:
https://portals.iucn.org/library/sites/library/files/documents/SSC-OP-052.pdf.
doi: 10.2305/IUCN.CH.2014.SSC-OP.52.en.
Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F.,
Taberlet, P., & Miaud, C. (2011). Persistence of environmental DNA in
freshwater ecosystems. PLoS ONE, 6, e23398. doi:
10.1371/journal.pone.0023398
De Ventura, L., Kopp, K., Seppälä, K., & Jokela, J. (2017). Tracing the
quagga mussel invasion along the Rhine river system using eDNA markers:
early detection and surveillance of invasive zebra and quagga mussels.Management of Biological Invasions, 8, 101–112. doi:
10.3391/mbi.2017.8.1.10
Donrovich, S., Douda, K., Plechingerova, V., Rylková, K., Horky, P.,
Slavík, O., Huan-zhang, L., Reichard, M., Lopes-Lima, M., & Sousa, R.
(2017). Invasive Chinese pond mussel Sinanodonta woodianathreatens native mussel reproduction by inducing crossresistance of host
fish. Aquatic Conservation Marine and Freshwater Ecosystems , 1-9.
doi: 10.1002/aqc.2759.
Duncan, N. (2008). Survey Protocol for Aquatic Mollusk Species:
Preliminary Inventory and Presence/Absence Sampling, Version 3.1.
Portland, OR. Interagency Special Status/Sensitive Species Program. U.S.
Department of Interior, Bureau of Land Management, Oregon/Washington and
U.S. Department of Agriculture, Forest Service, Region 6. Retrieved from
https://www.blm.gov/or/plans/surveyandmanage/files/10-mollusks_v3-1.pdf
Evans, N. T., Olds, B. P., Turner, C. R., Li, Y., Jerde, C. L., Mahon,
A. R., Pfrender, M. E., Lamberti, G. A., & Lodge, D. M. (2015).
Quantification of mesocosm fish and amphibian species diversity via eDNA
metabarcoding. Molecular Ecology Resources , 16, 29-41. doi:
10.1111/17550998.12433
Ficetola, G. F., Miaud, C., Pompanon, F., & Taberlet, P. (2008).
Species detection using environmental DNA from water samples.Biological Letters, 4, 423–425. doi: 10.1098/rsbl.2008.0118
Froufe, E., Lopes-Lima, M., Riccardi, N., Zaccara, S., Vanetti, I.,
Lajtner, J., Teixeira, A., Varandas, S., Prié, V., Zieritz, A., Sousa
R., & Bogan, A. E. (2017). Lifting the curtain on the freshwater mussel
diversity of the Italian Peninsula and Croatian Adriatic coast.Biodiversity and Conservation, 26, 3255-3274. doi:
10.1007/s10531-017-1403-z
Gargominy, O., Léonard, L., Prié, V., & Cucherat, X. (2016). De
l’utilité d’un inventaire national. MalaCo , 12 : 67-87.
Gargominy, O., Tercerie, S., Régnier, C., Ramage, T., Dupont, P.,
Daszkiewicz, P., & Poncet, L. (2019). TAXREF v13, référentiel
taxonomique pour la France : méthodologie, mise en œuvre et diffusion .
Retrieved from National Museum fop Natural History, Paris
https://inpn.mnhn.fr/docs-web/docs/download/302170
Goldberg, C. S., Sepulveda, A., Ray, A., Baumgardt J., & Waits, L. P.
(2013). Environmental DNA as a new method for early detection of New
Zealand mudsnails (Potamopyrgus antipodarum ). Freshwater
Science, 32, 792–800. doi: 10.1899/13-046.1
Huber, V., & Geist, J. (2019). Reproduction success of the invasiveSinanodonta woodiana (Lea 1834) in relation to native mussel
species. Biological Invasions , 21, 3451-3465. doi:
10.1007/s10530-019-02060-3.
Klymus, K. E., Marshall, N. T., & Stepien, C. A. (2017). Environmental
DNA (eDNA) metabarcoding assays to detect invasive invertebrate species
in the Great Lakes. PLoS ONE , 12(5), e0177643.
doi:10.1371/journal.pone.0177643
Liu, H.-P., Mitton, J. B., & Wu, S.-K. (1996). Paternal mitochondrial
DNA differentiation far exceeds maternal mitochondrial DNA and allozyme
differentiation in the freshwater mussel, Anodonta grandis
grandis . Evolution , 50, 952-957. doi:
10.1111/j.1558-5646.1996.tb03907.x
Lopes-Lima, M., Kebapçı, U., & Van Damme, D. (2014). Unio
crassus . The IUCN Red List of Threatened Species 2014:
e.T22736A42465628. doi:
10.2305/IUCN.UK.2014-1.RLTS.T22736A42465628.en. Downloaded on 28 April
2020.
Mioduchowska, M., Kaczmarczyk, A., Zajac, K., Zajac T., & Sell, J.
(2016). Gender-associated mitochondrial DNA heteroplasmy in somatic
tissues of the endangered freshwater mussel Unio crassus(bivalvia: unionidae): implications for sex identification and
phylogeographical studies. Journal of Experimental Zoology, 325A,
610–625. doi: 10.1002/jez.2055
Mouthon, J., & Kuiper, J. (1987). Inventaire des Sphaeriidae de France.
Paris, MNHN (Collection Inventaire de Faune et de Flore).
Mouthon, J., & Tair Abbaci, K. (2012). The taxonomic confusion
surrounding Pisidium (Bivalvia, Sphaeriidae): the possible birth
of a new taxon. Basteria 76 (4-6): 126-130
Mouthon, J., Forcellini, M., & van Haaren, T. (2018). Euglesa
compressa (Bivalvia, Sphaeriidae), native of North America, a ’hidden’
species introduced in Western Europe before 1940. Basteria,82(1-3), 50-54.
Mouthon, J., & Forcellini, M. (2017). Genetic evidence of the presence
in France of the North American species Euglesa compressa Prime,
1852, (Bivalvia, Sphaeriidae). BioInvasions Records, 6(3),
225-231. doi : 10.3391/bir.2017.6.3.07
Mouthon, J. (2018). Répartition en France des formes actuelle et fossile
d’Euglesa pulchella Jenyns , 1832 (Bivalvia, Sphaeriidae), une
espèce rare. Folia conchyliologica, 45, 3–8.
Pfenninger, M., Reinhardt, F., & Streit, B. (2002). Evidence for
cryptic hybridization between different evolutionary lineages of the
invasive clam genus Corbicula (Veneroida, Bivalvia).Journal of Evolutionary Biology , 15(5), 818-829. doi:
10.1046/j.1420-9101.2002.00440.x.
Pigneur, L.-M., Marescaux, J., Roland, K., Etoundi, E., Descy, J.-P., &
Van Doninck, K. (2011). Phylogeny and androgenesis in the invasiveCorbicula clams (Bivalvia, Corbiculidae) in western Europe.BMC Evolutionary Biology, 11, 147. doi: 10.1186/1471-2148-11-147
Pont, D., Rocle, M., Valentini, A., Civade, R., Jean, P., Maire, A.,
Roset, N., Schabuss, M., Zornig, H., & Dejean, T. (2018). Environmental
DNA reveals quantitative patterns of fish biodiversity in large rivers
despite its downstream transportation. Scientific Reports, 8,
10361. doi:10.1038/s41598-018-28424-8
Prie, V., Puillandre, N., & Bouchet, P. (2012). Bad taxonomy can kill:
molecular reevaluation of Unio mancus Lamarck, 1819 (Bivalvia:
Unionidae) and its accepted subspecies. Knowledge and Management
of Aquatic Ecosystems, 405(8). doi: 10.1051/kmae/2012014
Prié, V., & Puillandre, N. (2014). Molecular phylogeny, taxonomy and
distribution of French Unio species (Bivalvia, Unionidae).Hydrobiologia, 735(1), 95–110. doi : 10.1007/s10750-013-1571-0
Prié, V. (2017). Naïades et autres bivalves d’eau douce de France. Mèze,
Paris : Biotope éditions, Publications scientifiques du Muséum
(collection Inventaires et Biodiversité).
Prié, V., & Fruget, J.-F. (2017).
Heading south: new records of the invasive freshwater quagga musselDreissena rostriformis bugensis (Andrusov, 1897) in France and
further perspectives. Knowledge and Management of Aquatic
Ecosystems, 418, 37. doi: 10.1051/kmae/2017023
Prié, V., Soler, J., Araujo, R., Cucherat, X., Philippe, L., Legrand,
N., Patry, N., Adam, B., Jugé, P., Richard, N., & Wantzen, K. M.
(2018). Challenging exploration of troubled waters: ten years’ surveys
of the giant freshwater pearl mussel Margaritifera auricularia in
Europe. Hydrobiologia, 818(1), 157–175.
doi:10.1007/s10750-017-3456-0
Prié, V., Valentini, A., Lopes-Lima, M., Froufe, E., Rocle, M., Poulet,
N., Taberlet, P. & Déjean, T. (2020). Environmental DNA metabarcoding
for freshwater bivalves biodiversity assessment: methods and results for
the Western Palearctic (European sub-region). Hydrobiologia . doi:
10.1007/s10750-020-04260-8
Riccardi, N., Froufe, E., Bogan, A. E., Zieritz, A., Teixeira, A.,
Vanetti, I., Varandas, S., Zaccara, S., Nagel, K.-O., & Lopes-Lima, M.
(2019). Phylogeny of European Anodontini (Bivalvia: Unionidae) with a
redescription of Anodonta exulcerata . Zoological Journal of
the Linnean Society , zlz136. doi: 10.1093/zoolinnean/zlz136.
Stoeckle, B. C., Huehn, R., & Geist, J. (2016). Environmental DNA as a
monitoring tool for the endangered freshwater pearl mussel
(Margaritifera margaritifera L.): a substitute for classical
monitoring approaches? Aquatic Conservation Marine and Freshwater
ecosystems, 26(6), 1120–1129. doi: 10.1002/aqc.2611
Schnell, I. B., Bohmann, K., & Gilbert, M. T. (2015). Tag jumps
illuminated – reducing sequence‐to‐sample misidentifications in
metabarcoding studies. Molecular Ecology Resources, 15,
1289–1303. doi:10.1111/1755-0998.12402
Taberlet, P., Coissac, E., Hajibabaei, M., & Rieseberg, L. H. (2012).
Environmental DNA. Molecular Ecology, 21, 1789–1793. doi:
10.1111/j.1365-294X.2012.05542.x
Thomsen, P. F., & Willerslev, E. (2015). Environmental DNA – an
emerging tool in conservation for monitoring past and present
biodiversity. Biological Conservation, 183, 4-18. doi:
10.1016/j.biocon.2014.11.019
Welter-Schultes, F. (2012). European non-marine molluscs, a guide for
species identification. Göttingen: Planet Poster Editions.
Zouros, E., Ball, A.O., Saavedra, C., & Freeman, K. R. (1994).
Mitochondrial DNA inheritance. Nature, 368(818). doi:
10.1038/368818a0